Publications by authors named "Ivan Jakovlic"

Article Synopsis
  • Studies on mitochondrial genome evolution show varying results, particularly in flatworms, which have the fastest-evolving mitogenomic sequences among bilaterians.
  • Researchers analyzed 223 flatworm species using phylogenetic models, finding that factors like thermic host environment and longevity had minimal effect on sequence evolution and genome size.
  • The study highlights that parasitism significantly explains branch length variability in flatworms, with free-living turbellaria evolving more quickly than parasitic Neodermata, suggesting the need to consider lineage-specific factors and the episodic nature of evolutionary changes in these analyses.
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Background: Gyrodactylus is a lineage of monogenean flatworm ectoparasites exhibiting many features that make them a suitable model to study the host-parasite coevolutionary dynamics. Previous coevolutionary studies of this lineage mainly relied on low-power datasets (a small number of samples and a single molecular marker) and (now) outdated algorithms.

Methods: To investigate the coevolutionary relationship of gyrodactylids and their fish hosts in high resolution, we used complete mitogenomes (including two newly sequenced Gyrodactylus species), a large number of species in the single-gene dataset, and four different coevolutionary algorithms.

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The genomic evolution of Polyopisthocotylea remains poorly understood in comparison to the remaining three classes of Neodermata: Monopisthocotylea, Cestoda, and Trematoda. Moreover, the evolutionary sequence of major events in the phylogeny of Neodermata remains unresolved. Herein we sequenced the mitogenome and transcriptome of the polyopisthocotylean Diplorchis sp.

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The evidence that parasitic animals exhibit elevated mitogenomic evolutionary rates is inconsistent and limited to Arthropoda. Similarly, the evidence that mitogenomic evolution is faster in species with low locomotory capacity is limited to a handful of animal lineages. We hypothesised that these two variables are associated and that locomotory capacity is a major underlying factor driving the elevated rates in parasites.

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Background: Acanthocephala is a clade of obligate endoparasites whose mitochondrial genomes (mitogenomes) and evolution remain relatively poorly understood. Previous studies reported that atp8 is lacking from acanthocephalan mitogenomes, and that tRNA genes often have nonstandard structures. Heterosentis pseudobagri (Arhythmacanthidae) is an acanthocephalan fish endoparasite for which no molecular data are currently available, and biological information is unavailable in the English language.

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Phylogenetic analysis has entered the genomics (multilocus) era. For less experienced researchers, conquering the large number of software programs required for a multilocus-based phylogenetic reconstruction can be somewhat daunting and time-consuming. PhyloSuite, a software with a user-friendly GUI, was designed to make this process more accessible by integrating multiple software programs needed for multilocus and single-gene phylogenies and further streamlining the whole process.

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The arms race between humans and pathogens drives the evolution of the human genome. It is thus expected that genes from the interferon-regulatory factors family (IRFs), a critical family for anti-viral immune response, should be undergoing episodes of positive selection. Herein, we tested this hypothesis and found multiple lines of evidence for positive selection on the amino acid site Val129 (NP_006075.

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Article Synopsis
  • The study focuses on the mitochondrial genome of the fish parasite Pseudocapillaria tomentosa, which shows a unique structure compared to other nematodes within the Enoplea class.
  • P. tomentosa has significantly reduced noncoding regions and an inverted GC skew, indicating evolutionary divergence from the ancestral mitogenome architecture.
  • The research finds that while some lineages maintain a conserved mitochondrial structure, others exhibit substantial architectural variations, highlighting a discontinuous evolution pattern in enoplean nematodes.
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Article Synopsis
  • - Systemic lupus erythematosus (SLE) is a rare autoimmune disease affecting about 0.1% of the population, with prior research revealing common variants but lacking studies on rare variants among Chinese patients using whole-genome sequencing (WGS).
  • - This study identified novel rare protein-coding gene variants in SLE patients, showing that the burden of rare variants was significantly higher than common variants, indicating their larger impact on SLE development.
  • - Specific rare missense variants in the WNT16 and ERVW-1 genes were linked to the disease, demonstrating significant associations absent in controls, and functional assays indicated that mutant forms of these genes failed to activate essential pathways, supporting their role in SLE
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In mammals, bile acid (BA) concentrations are regulated largely by the gut microbiota, and a study has shown that some metabolic responses to the gut microbiota are conserved between zebrafish and mice. However, it remains unknown whether the influence of specific intestinal microbes on BA metabolism is conserved between higher and lower vertebrates (i.e.

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Base composition skews (G-C/G+C) of mitochondrial genomes are believed to be primarily driven by mutational pressure, which is positively correlated with metabolic rate. In marine animals, metabolic rate is also positively correlated with locomotory capacity. Given the central role of mitochondria in energy metabolism, we hypothesised that selection for locomotory capacity should be positively correlated with the strength of purifying selection (dN/dS), and thus be negatively correlated with the skew magnitude.

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Inversions of the origin of replication (ORI) in mitochondrial genomes produce asymmetrical mutational pressures that can cause strong base composition skews. Due to skews often being overlooked, the total number of crustacean lineages that underwent ORI events remains unknown. We analysed skews, cumulative skew plots, conserved sequence motifs, and mitochondrial architecture of all 965 available crustacean mitogenomes (699 unique species).

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Background: The Muscovy duck (Cairina moschata) is an economically important duck species, with favourable growth and carcass composition parameters in comparison to other ducks. However, limited genomic resources for Muscovy duck hinder our understanding of its evolution and genetic diversity.

Results: We combined linked-reads sequencing technology and reference-guided methods for de novo genome assembly.

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Background: Argeia pugettensis is an isopod species that parasitizes other crustaceans. Its huge native geographic range spans the Pacific from China to California, but molecular data are available only for a handful of specimens from North-American populations. We sequenced and characterised the complete mitogenome of a specimen collected in the Yellow Sea.

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The majority strand of mitochondrial genomes of crustaceans usually exhibits negative GC skews. Most isopods exhibit an inversed strand asymmetry, believed to be a consequence of an inversion of the replication origin (ROI). Recently, we proposed that an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families resulted in a double-inverted skew (negative GC), and that taxa with homoplastic skews cluster together in phylogenetic analyses (long-branch attraction, LBA).

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Article Synopsis
  • The mitogenome of GL, a species from the high-altitude Qinghai-Tibet Plateau, shows adaptations to extreme environments compared to GP, which lives at lower altitudes.
  • Both mitogenomes share a conserved structure but have low gene identity, indicating significant genetic divergence.
  • The evolutionary pressures on GL and GP are different, with GL undergoing strong purifying selection while GP faces directional or relaxed selection, suggesting GP may have experienced recent speciation and unique mutational pressures.
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The oriental river prawn, Macrobrachium nipponense, is a commercial freshwater prawn species in China. It is highly sensitive to hypoxia, and this has posed a challenge to its intensive culturing. To date, the effects of hypoxia on reproduction in female prawns are not entirely clear, as are the underlying mechanisms of the effects of hypoxia.

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Background: Species belonging to the genus Lernaea are cosmopolitan parasites that can infect many different freshwater fish hosts. Due to a high degree of morphological intraspecific variability and high levels of interspecific similarities, their classification is extremely difficult and controversial. Although the suitability of the shape of cephalic horns has been questioned decades ago by some experimental infection studies, this character still plays the central role in the identification of Lernaea spp.

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Due to the incongruence of morphology-based hypotheses and scarcity of molecular data, validity of the order Tetraonchidea remains contentious. The only complete mitogenome currently available for the entire order is that of Paratetraonchoides inermis (Tetraonchoididae). To study the phylogeny of Tetraonchidea from mitogenomic perspective, we sequenced the first mitogenome for the family Tetraonchidae: Tetraonchus monenteron (Tetraonchidea).

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Whereas a majority of monogenean flatworms are ectoparasitic, i.e., parasitize on external surfaces (mainly gills) of their fish hosts, species (subfamily Ancyrocephalinae) are mesoparasitic, i.

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Multigene and genomic data sets have become commonplace in the field of phylogenetics, but many existing tools are not designed for such data sets, which often makes the analysis time-consuming and tedious. Here, we present PhyloSuite, a (cross-platform, open-source, stand-alone Python graphical user interface) user-friendly workflow desktop platform dedicated to streamlining molecular sequence data management and evolutionary phylogenetics studies. It uses a plugin-based system that integrates several phylogenetic and bioinformatic tools, thereby streamlining the entire procedure, from data acquisition to phylogenetic tree annotation (in combination with iTOL).

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Dietary betaine supplementation notably ameliorated fatty liver disease caused by high dietary carbohydrate. We hypothesised that the mechanism behind this is the alteration of bile acid and trimethylamine-N-oxide (TMAO) metabolism. We further explored this mechanism by supplementing betaine (1%) to the diet of a farmed fish Megalobrama amblycephala.

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Phylogenetic framework for the closely related Ancylodiscoidinae and Ancyrocephalinae subfamilies remains contentious. As this issue was never studied using a large molecular marker, we sequenced the first two Ancylodiscoidinae mitogenomes: and . Both mitogenomes had two non-coding regions (NCRs) that contained a number of repetitive hairpin-forming elements (RHE).

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Recent mitogenomic studies have exposed a gene order (GO) shared by two classes, four orders and 31 species ('common GO') within the flatworm subphylum Neodermata. There are two possible hypotheses for this phenomenon: convergent evolution (homoplasy) or shared ancestry (plesiomorphy). To test those, we conducted a meta-analysis on all available mitogenomes to infer the evolutionary history of GO in Neodermata.

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